Chemical systems for the oxidative cleavage of DNA have been developed and used in recent years (Dervan, 1986; Youngquist et al., 1987; Sluka et al., 1987; Strobel et al., 1990; Chen et al., 1986; Francois et al., 1989; Ebright et al., 1990; Bruice et al., 1991; Sigman et al., 1990; Chen et al., 1987). For example, phenanthroline attached to an oligonucleotide or polypeptide will bind cupric ion and this complex can be used to cleave DNA. In the presence of a reducing agent the bound cupric ion is reduced to cuprous ion, which reduces molecular oxygen to produce hydrogen peroxide. The H.sub.2 O.sub.2 reacts with the cuprous complex to form a copper-oxo species that is directly responsible for cleavage. Chen et al. (1987) used this approach to convert the E. coli trp repressor to a site-specific deoxyribonuclease.
Copper-phenanthrolene has also been tethered to oligonucleotides to induce sequence-specific cleavage of single-stranded and double-stranded DNA (Frangois et al., 1989). An alternative but chemically analogous system (Dreyer et al., 1985; Dervan, 1986; Moser et al., 1987; Maher et al., 1989) utilizes EDTA-chelated iron tethered to an oligonucleotide to cleave DNA. By attaching an Fe-EDTA group to the DNA-binding domain of the Hin recombinase, Sluka et al. (1987) achieved site-specific DNA cleavage at Hin recombination sites.
In addition to the above chemical systems for the oxidative cleavage of DNA, Corey and Schultz (1987) have converted the nonspecific nuclease staphylococcal nuclease to a site-specific nuclease by attaching it to an oligonucleotide. In this hybrid molecule, the relatively short oligonucleotide is able to confer binding specificity on the target DNA via hybridization (Corey et al., 1987) or triplex formation (Pei et al., 1990).
Although the conversion of DNA-binding molecules to site-specific chemical deoxyribonucleases has been an area of active investigation, efforts to achieve site-specific cleavage of RNA have been mainly limited to the use of ribozymes. Experiments performed in support of the present invention have demonstrated site-specific cleavage of RNA using sequence specific RNA binding proteins.